ATAC-seq of Phytophthora infestans T30-4 mycelium

Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that leads to Irish potato famine and threatens world-wide food security. Despite the genome of P. infestans has provided fundamental resource for studying the aggressiveness of this pandemic pathogen, the epigenomes remain poorly understood. Here, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we demonstrate post-translational modifications (PTM) at P. infestans core histone H3. The PTMs not only include these prevalent modifications in eukaryotes, and also some novel marks, such as H3K53me2 and H3K122me3. We focused on the trimethylations of H3K4, H3K9 and H3K27 and H3K36, and profiled P. infestans epigenomes employing Native Chromatin Immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromomatin accessibility by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3, and are generally in condense chromatin. Interestingly, we observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions that barely have the four histone modifications. With a combination of genomic, epigenomic, transcriptomic strategies, our study illustrates the epigenetic states in P. infestans, which will help to study genomic functions and regulations in this pathogen. Two replicates of P. infestans T30-4 mycelium stage sample were performed.

致病疫霉（Phytophthora infestans）是马铃薯晚疫病的致病菌，曾引发爱尔兰马铃薯饥荒，是一类极具破坏性的植物病原，威胁全球粮食安全。尽管致病疫霉的基因组为解析该流行性病原的致病特性提供了基础研究资源，但学界对其表观基因组的认知仍较为匮乏。本研究借助液相色谱-串联质谱（LC-MS/MS），鉴定出致病疫霉核心组蛋白H3的翻译后修饰（PTM）：这些修饰不仅包含真核生物中普遍存在的类型，还包括H3K53me2、H3K122me3等新型修饰位点。研究重点聚焦于H3K4、H3K9、H3K27及H3K36的三甲基化修饰，并通过原生染色质免疫沉淀测序（N-ChIP-seq）绘制了致病疫霉的表观基因组图谱。同时，本研究利用高通量测序转座酶可及性染色质分析（ATAC-seq）定位了致病疫霉的染色质可及性区域。研究发现，适应性基因组区域的H3K9me3与H3K27me3修饰水平显著更高，且通常处于染色质浓缩状态。值得注意的是，编码效应蛋白等毒力因子的基因富集于几乎不含上述四种组蛋白修饰的开放染色质区域。本研究结合基因组学、表观基因组学与转录组学策略，阐明了致病疫霉的表观遗传状态，将为该病原的基因组功能与调控机制研究提供重要参考。本研究设置了两份致病疫霉T30-4菌株菌丝体阶段的生物学重复样本。